# nnUNet/nnunetv2/inference/predict_from_raw_data.py
# nnUNet/documentation/how_to_use_nnunet.md
# nnUNetv2_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -d DATASET_NAME_OR_ID -c CONFIGURATION --save_probabilities
import subprocess
import os
os.environ["nnUNet_raw"] = "nnUNetFrame/DATASET/nnUNet_raw"
os.environ["nnUNet_preprocessed"] = "nnUNetFrame/DATASET/nnUNet_preprocessed"
os.environ["nnUNet_results"] = "nnUNetFrame/DATASET/nnUNet_results"

subprocess.check_call(["Depend/Scripts/nnUNetv2_predict",
                       "-i", "nnUNetFrame/DATASET/nnUNet_raw/Dataset004_Hippocampus/imagesTs",
                       "-o", "nnUNetFrame/DATASET/user_download/004_output",
                       '-d', '4',
                       '-c', '3d_fullres',
                       '-f', '0'])
